--- trunk/electrostaticMethodsPaper/electrostaticMethods.tex	2006/03/07 20:46:45	2604
+++ trunk/electrostaticMethodsPaper/electrostaticMethods.tex	2006/03/08 15:14:20	2605
@@ -11,6 +11,8 @@
 \usepackage{tabularx}
 \usepackage{graphicx}
 \usepackage{booktabs}
+\usepackage{bibentry}
+\usepackage{mathrsfs}
 %\usepackage{berkeley}
 \usepackage[ref]{overcite}
 \pagestyle{plain}
@@ -35,8 +37,9 @@ Notre Dame, Indiana 46556}
 
 \maketitle
 %\doublespacing
-
+\nobibliography{}
 \begin{abstract}
+A new method for accumulating electrostatic interactions was derived from the previous efforts described in \bibentry{Wolf99} and \bibentry{Zahn02} as a possible replacement for lattice sum methods in molecular simulations.  Comparisons were performed with this and other pairwise electrostatic summation techniques against the smooth particle mesh Ewald (SPME) summation to see how well they reproduce the energetics and dynamics of a variety of simulation types.  The newly derived Shifted-Force technique shows a remarkable ability to reproduce the behavior exhibited in simulations using SPME with an $\mathscr{O}(N)$ computational cost, equivalent to merely the real-space portion of the lattice summation.  
 \end{abstract}
 
 %\narrowtext 
@@ -47,7 +50,7 @@ Notre Dame, Indiana 46556}
 
 \section{Introduction}
 
-In molecular simulations, proper accumulation of the electrostatic interactions is considered one of the most essential and computationally demanding tasks.  The strength and slow decay of the electrostatics are what give rise to their problematic importance.
+In molecular simulations, proper accumulation of the electrostatic interactions is considered one of the most essential and computationally demanding tasks.  
 
 blah blah blah Ewald Sum Important blah blah blah
 
@@ -101,7 +104,7 @@ By studying these methods in systems composed entirely
 
 \section{Methods}
 
-In each of the simulated systems, 500 distinct configurations were generated, and the electrostatic summation methods were compared via sequential application on each of these fixed configurations.  The methods compared include SPME, the aforementioned Shifted Potential and Shifted Force methods - both with damping parameters ($\alpha$) of 0, 0.1, 0.2, and 0.3 \AA$^{-1}$, reaction field with an infinite dielectric constant, and an unmodified cutoff.  Group-based cutoffs with a fifth-order polynomial switching function were necessary for the reaction field simulations and were utilized in the SP, SF, and pure cutoff methods for comparison to the standard lack of group-based cutoffs with a hard truncation.  The SPME calculations were performed using the TINKER implementation of SPME, while all all other method calculations were performed using the OOPSE molecular mechanics package.\cite{Ponder87,Meineke05}
+In each of the simulated systems, 500 distinct configurations were generated, and the electrostatic summation methods were compared via sequential application on each of these fixed configurations.  The methods compared include SPME, the aforementioned Shifted Potential and Shifted Force methods - both with damping parameters ($\alpha$) of 0, 0.1, 0.2, and 0.3 \AA$^{-1}$ (no, light, moderate, and heavy damping respectively), reaction field with an infinite dielectric constant, and an unmodified cutoff.  Group-based cutoffs with a fifth-order polynomial switching function were necessary for the reaction field simulations and were utilized in the SP, SF, and pure cutoff methods for comparison to the standard lack of group-based cutoffs with a hard truncation.  The SPME calculations were performed using the TINKER implementation of SPME, while all all other method calculations were performed using the OOPSE molecular mechanics package.\cite{Ponder87,Meineke05}
 
 Generation of the system configurations was dependent on the system type.  For the solid and liquid water configurations, configuration snapshots were taken at regular intervals from higher temperature 1000 SPC/E water molecule trajectories and each equilibrated individually.  The solid and liquid NaCl systems consisted of 500 Na+ and 500 Cl- ions and were selected and equilibrated in the same fashion as the water systems.  For the low and high ionic strength NaCl solutions, 4 and 40 ions were first solvated in a 1000 water molecule boxes respectively.  Ion and water positions were then randomly swapped, and the resulting configurations were again equilibrated individually.  Finally, for the Argon/Water "charge void" systems, the identities of all the SPC/E waters within 6 \AA\ of the center of the equilibrated water configurations were converted to argon (Fig. \ref{fig:argonSlice}).
 
@@ -148,7 +151,7 @@ While studying the energy differences provides insight
 \label{fig:frcMag}
 \end{figure}
 
-The results in figure \ref{fig:frcMag} for the most part parallel those seen in the previous look at the $\Delta E$ results.  The unmodified cutoff results are poor, but using group based cutoffs and a switching function provides a improvement much more significant than what was seen with $\Delta E$.  Looking at the Shifted Potential sets, the slope and R$^2$ improve with the use of damping to an optimal result of 0.2 \AA $^{-1}$ for the 12 and 15 \AA\ cutoffs.  Further increases in damping, while beneficial for simulations with a cutoff radius of 9 \AA\ , is detrimental to simulations with larger cutoff radii.  The undamped Shifted Force method gives forces in line with those obtained using SPME, and use of a damping function results in minor improvement.  The reaction field results are surprisingly good, considering the poor quality of the fits for the $\Delta E$ results.  There is still a considerable degree of scatter in the data, but it correlates well in general.
+The results in figure \ref{fig:frcMag} for the most part parallel those seen in the previous look at the $\Delta E$ results.  The unmodified cutoff results are poor, but using group based cutoffs and a switching function provides a improvement much more significant than what was seen with $\Delta E$.  Looking at the Shifted Potential sets, the slope and $R^2$ improve with the use of damping to an optimal result of 0.2 \AA $^{-1}$ for the 12 and 15 \AA\ cutoffs.  Further increases in damping, while beneficial for simulations with a cutoff radius of 9 \AA\ , is detrimental to simulations with larger cutoff radii.  The undamped Shifted Force method gives forces in line with those obtained using SPME, and use of a damping function results in minor improvement.  The reaction field results are surprisingly good, considering the poor quality of the fits for the $\Delta E$ results.  There is still a considerable degree of scatter in the data, but it correlates well in general.
 
 \subsection{Torque Magnitude Comparison}
 
@@ -216,7 +219,7 @@ Both the force and torque $\sigma^2$ results from the 
    \label{tab:groupAngle}
 \end{table}
 
-Although not discussed previously, group based cutoffs can be applied to both the Shifted Potential and Force methods.  Use off a switching function corrects for the discontinuities that arise when atoms of a group exit the cutoff before the group's center of mass.  Though there are no significant benefit or drawbacks observed in $\Delta E$ and vector magnitude results when doing this, there is a measurable improvement in the vector angle results.  Table \ref{tab:groupAngle} shows the angular variance values obtained using group based cutoffs and a switching function alongside the standard results seen in figure \ref{frcTrqAng} for comparison purposes.  The Shifted Potential shows much narrower angular distributions for both the force and torque vectors when using an $\alpha$ of 0.2 \AA$^{-1}$ or less, while Shifted Force shows improvements in the undamped and lightly damped cases.  Thus, by calculating the electrostatic interactions in terms of molecular pairs rather than atomic pairs, the direction of the force and torque vectors are determined more accurately.  
+Although not discussed previously, group based cutoffs can be applied to both the Shifted Potential and Force methods.  Use off a switching function corrects for the discontinuities that arise when atoms of a group exit the cutoff before the group's center of mass.  Though there are no significant benefit or drawbacks observed in $\Delta E$ and vector magnitude results when doing this, there is a measurable improvement in the vector angle results.  Table \ref{tab:groupAngle} shows the angular variance values obtained using group based cutoffs and a switching function alongside the standard results seen in figure \ref{fig:frcTrqAng} for comparison purposes.  The Shifted Potential shows much narrower angular distributions for both the force and torque vectors when using an $\alpha$ of 0.2 \AA$^{-1}$ or less, while Shifted Force shows improvements in the undamped and lightly damped cases.  Thus, by calculating the electrostatic interactions in terms of molecular pairs rather than atomic pairs, the direction of the force and torque vectors are determined more accurately.  
 
 One additional trend to recognize in table \ref{tab:groupAngle} is that the $\sigma^2$ values for both Shifted Potential and Shifted Force converge as $\alpha$ increases, something that is easier to see when using group based cutoffs.  Looking back on figures \ref{fig:delE}, \ref{fig:frcMag}, and \ref{fig:trqMag}, show this behavior clearly at large $\alpha$ and cutoff values.  The reason for this is that the complimentary error function inserted into the potential weakens the electrostatic interaction as $\alpha$ increases.  Thus, at larger values of $\alpha$, both the summation method types progress toward non-interacting functions, so care is required in choosing large damping functions lest one generate an undesirable loss in the pair interaction.  Kast \textit{et al.}  developed a method for choosing appropriate $\alpha$ values for these types of electrostatic summation methods by fitting to $g(r)$ data, and their methods indicate optimal values of 0.34, 0.25, and 0.16 \AA$^{-1}$ for cutoff values of 9, 12, and 15 \AA\ respectively.\cite{Kast03}  These appear to be reasonable choices to obtain proper MC behavior (Fig. \ref{fig:delE}); however, based on these findings, choices this high would introduce error in the molecular torques, particularly for the shorter cutoffs.  Based on the above findings, empirical damping up to 0.2 \AA$^{-1}$ proves to be beneficial, but is  arguably unnecessary when using the Shifted-Force method.
 
@@ -229,9 +232,9 @@ C_v(t) = \langle v_i(0)\cdot v_i(t)\rangle.
 C_v(t) = \langle v_i(0)\cdot v_i(t)\rangle.
 \label{eq:vCorr}
 \end{equation}
-Velocity autocorrelation functions require detailed short time data and long trajectories for good statistics, thus velocity information was saved every 5 fs over 100 ps trajectories.  The power spectrum ($F_t$) is obtained via discrete Fourier transform of the autocorrelation function
+Velocity autocorrelation functions require detailed short time data and long trajectories for good statistics, thus velocity information was saved every 5 fs over 100 ps trajectories.  The power spectrum ($I(\omega)$) is obtained via discrete Fourier transform of the autocorrelation function
 \begin{equation}
-F_t = \sum^{N-1}_{\omega=0}C_v(t)e^{-i\omega t/N}, 
+I(\omega) = \sum^{N-1}_{\omega=0}C_v(t)e^{-i\omega t/N}, 
 \label{eq:powerSpec}
 \end{equation}
 where $N$ is the number of time samples in $C_v(t)$ and the frequency, $\omega=0,\ 1,\ ...,\ N-1$.  The resulting spectra (Fig. \ref{fig:normalModes}) show the normal mode frequencies for the crystal under the simulated conditions.
@@ -251,14 +254,18 @@ where $S(r)$ is a switching function that smoothly zer
 \begin{figure}
 \centering
 \includegraphics[width = 3.25in]{./alphaCompare.pdf}
-\caption{}
+\caption{Normal modes for an NaCl crystal at 1000 K when using SPME and a simple damped Coulombic sum with damping coefficients ($\alpha$)ranging from 0.15 to 0.3 \AA$^{-1}$.  As $\alpha$ increases, the normal modes are red-shifted towards and eventually beyond the values given by SPME.  The larger $\alpha$ values weaken the real-space electrostatics, explaining this shift towards less strongly correlated motions in the crystal.}
 \label{fig:dampInc}
 \end{figure}
 
 \section{Conclusions}
 
-This investigation of pairwise electrostatic summation techniques shows that there are viable and more computationally efficient electrostatic summation techniques than the Ewald summation, chiefly methods derived from the damped Coulombic sum originally proposed by Wolf \textit{et al.}\cite{Wolf99,Zahn02}  In particular, the Shifted-Force method reformulated above
+This investigation of pairwise electrostatic summation techniques shows that there are viable and more computationally efficient electrostatic summation techniques than the Ewald summation, chiefly methods derived from the damped Coulombic sum originally proposed by Wolf \textit{et al.}\cite{Wolf99,Zahn02}  In particular, the Shifted-Force method, reformulated above, shows a remarkable ability to reproduce the energetic and dynamic characteristics exhibited by simulations employing lattice summation techniques.  The cumulative energy difference results showed the undamped Shifted-Force and moderately damped Shifted-Potential methods produced results nearly identical to SPME.  Similarly for the dynamic features, the un- to moderately damped Shifted-Force and moderately damped Shifted-Potential methods produce force and torque vector magnitude and directions very similar to the expected values.  These results translate into long-time dynamic behavior equivalent to that produced in simulations using SPME.
 
+Aside from the computational cost benefit, these techniques have applicability in situations where the use of the Ewald sum can prove problematic.  Primary among them is their use in interfacial systems, where the unmodified lattice sum techniques artificially accentuate the periodicity of the system in an undesirable manner.  There have been alterations to the standard Ewald techniques, via corrections and reformulations, to compensate for these systems; but these pairwise techniques require no modifications, making them natural tools to tackle these problems.  Additionally, this transferability gives it benefits over other pairwise methods, like reaction field, because estimations of physical properties, like the dielectric constant, are unnecessary.
+
+These results don't deprecate the use of the Ewald summation; in fact, it is the standard to which these simple pairwise sums are judged.  However, these results do speak to the necessity of the Ewald summation in all molecular simulations.  That a simple pairwise technique can be substituted to gain nearly all the physical effects provided by the full lattice sum makes us question whether the minimal perturbations bestowed through added complexity and increased cost are worth it.
+
 \section{Acknowledgments}
 
 \newpage 
